Even as he was composing his Chile notes, Darwin was turning his mind west, for the Beagle, having finished its laborious survey of the South American coast, was making ready to sail. Examining charts of the route ahead, Darwin contemplated the oddity that is the Pacific: a broad pan, immensely deep, with arcs and ovals and doglegs of coral isles rising, as he put it, from its “profoundest parts.” Several of these archipelagos — the Galapagos, the Tuamotus, French Polynesia, the Fijis and the Friendlys — lay along the Beagle‘s route. In the 60 years since Captain James Cook had mapped them, these islands had commanded much interest among geologists and naturalists. They were intrigued by the great depths from which they rose; by their volcanic nature; by their ordered but irregular arrangements, like pearl necklaces tossed to the floor; and by the islands’ distinctive annularity.

Someone excited sleepless by geology wasn’t likely to resist such shapes. Darwin’s Andean wanderings and ruminations had fired what would prove an insatiable appetite for discovering patterns spanning space and time. These ringed islands presented precisely such a pattern.

The puzzle seemed ripe for solution. Though coral islands and reefs had intrigued Europe’s scientists and public for almost a century (an interest greatly boosted by the descriptions Cook brought back of the South Pacific archipelagos in the 1770s), no one had plausibly explained how they came to be. They were initially appreciated mainly for the sheer wonder of their existence, apparently climbing from the sea’s depths to create new landscapes. In the eighteenth-century fascination with the idea of a Great Chain of Being, corals held a special place for seeming to bridge the gap between plant and animal, and after Jean-Andre Peyssonnel showed them to be animals in 1753, for creating with their calcified skeletons the huge structures that joined the organic and the inorganic worlds as well as sea and land. In the early nineteenth century, some saw in coral reefs a welcome antidote to the erosion that Huttonian geology saw as erasing humankind’s terrestrial platform. “Whatever destroying tendencies … exist on the earth,” wrote one prominent geologist in 1818, “these renovating powers compensate for them.”

Such speculations rose naturally when geology was so young, the reefs so many, and scientific visits to them so few and brief. Naturalists on the Cook and other expeditions of the late 1700s, however, began to fill in the blanks. They established that the reefs were formed by the accumulating skeletons of huge colonies of tiny, tube-shaped animals known as coral polyps. These polyps, which would later be found to be tiny, hard-bodied cousins of sea anenomes, were also variously referred to as insects, “molluscus worms,” insects, or even “animalcules.” They seemed to live only in warm tropical waters, generally no further than 25 or 30 degrees of the equator. The polyps apparently built their great works extremely slowly. No one who lived in coral regions described discernible growth, and while nineteenth-century European visitors comparing the reefs to descriptions and charts made the previous century found some reef areas apparently torn up by storms, they could not find measurable expansion. At first it was thought that the reefs might build themselves up from seabottom as deep as several hundred or even several thousand feet. But by 1820 it had been established that corals grew only in water no more than 100 or 200 feet deep.

These observations presented two critical mysteries. One was how shallow-water animals came to grow on platforms that rose from the Pacific’s greatest depths. Did they just happen to find these plateaus, or did they somehow build them? The other puzzle was the distinctive annularity of reefs surrounding islands, of many coral islands themselves, and even of the vast coral atolls, or groups of islands, that were strung around the Pacific. The reefs surrounding islands followed their contours, often ringing them with a calm lagoon between reef and shore. Other reefs surrounded lagoons only, with no island in the lagoon’s center. And the Pacific’s many atolls – collections of smaller coral islands — often took ringlike or looplike forms themselves. With so many reefs and atolls taking circular and ovoid forms, it seemed unlikely that reefs just happened to grow on convenient platforms. Some dynamic relationship between the reefs and their foundations seemed to shape them.

The first coral reef theories, offered in the late 1700s and early 1800s, gave fairly simplistic or teleological answers to these questions. For instance, J.R. Forster, the naturalist on Cook’s second voyage in the mid-1770s, proposed that corals simply knew they needed to build a circular structure to give themselves a sheltered environment. Another early theory, that of the naturalist and vulcanist Christian Leopold von Buch (1774-1853), had coral reefs growing on the rims of “elevation craters” that had formed when huge, gaseous blisters — quite distinct from volcanoes — raised the sea bottom and then popped and collapsed. This theory, which ignored the fact that every major known reef area lay in volcanic areas, was a strange one coming from von Buch, for he was a noted vulcanist, having firmly established, early in the 1800s, that lava formed new rock. Von Buch’s discovery of the volcanic nature of rock greatly advanced uniformitarianism, for catastrophist theory had maintained that all the earth’s rocks and land had long before precipitated from a primordial ocean. Yet this pioneering vulcanist overlooked the seemingly obvious connection between coral reefs and volcanoes. A few other reef scientists, citing what seemed plain in Caribbean and Atlantic reefs, which rose from shallower depths, offered that most reef platforms consist of current-deposited sediment.

The first theory to get wide acceptance, however, was that of Johann Eschscholtz, who visited the Marshall Islands on an 1815-1818 Russian voyage led by Otto von Kotzebue. Eschscholtz hypothesized that corals grow faster to seaward, responding ot the influx of oxygen and food, and so that as they rise on existing platforms (as he saw it), they slowly create a bulwark that increasingly grows faster on its sea-facing side. They grow from the center outward, in other words. This, he explained, creates a tendency toward annularity that, along with the shape of the platforms they grew on, accounts for each reef’s form. Though Eschscholtz overextended this idea to unlikely deeps because the depth limit of coral growth wasn’t established until just after he offered his theory, his hypothesis seemed to account for many reef forms and helped to explain lagoons.

Eschscholtz experienced mixed luck with this theory. While his reef-building model exerted immense influence, it was incorrectly attributed for 75 years (50 years beyond Eschscholtz’s death) to his colleague on Kotzebue’s voyage, a poet-naturalist named Chamisso. In any event, the Chamisso-Eschscholtz hypothesis, especially its assertion that coral reefs grow faster to the seaward, shaped thinking about reefs for a century, giving rise to many other theories.

Foremost among these other theories, and the one that came closest to enjoying a consensus in the early 1800s, was what might be called an elevated-volcano theory. This held that most of the world’s coral reefs grew on volcanic mountaintops that had risen close to the surface, presumably lifted by mountain-building surfaces similar to those on land,, and then expired, leaving the round ring of the volcano’s mouth near the surface. The round shape of many islands and atolls supported this idea, as did existence of old coral on some islands lifted well out of the water. For how would those corals have reached terrestrial mountaintops if the mountains hadn’t been pushed from below the surface?

This raised-volcano hypothesis, as it happens, was the one backed by Lyell and presented in Principles of Geology as the most authoritative explanation. This theory held weaknesses too, however, and Darwin, pondering the charts in Chile, found them conclusively damning. Yes, he recognized, many isles had risen well above the surface, suggesting elevation. But the charts showed that those taller islands were vastly outnumbered by the thousands of coral isles and atolls, including archipelagos hundreds of miles long, that barely cleared the water. The above-water portions of these low structures were clearly created by coral debris and sand being tossed atop subsurface reefs. Was he to accept that the foundations of all these isles had conveniently risen to within a couple hundred feet of waterline and then stopped growing so that coral could complete the trip? Hardly. As he put it in the Voyage of the Beagle,

It is [highly] improbable that the elevatory forces should have uplifted throughout … vast areas, innumerable great rocky banks within 20 to 30 fathoms … of the surface of the sea, and not one single point above that level; for where on the whole surface of the globe can we find a single chain of mountains, even a few hundred miles in length, with their many summits rising within a few feet of a given level, and not one pinnacle above it?

Besides, he noted, the span of many atolls, some of them rough circles dozens of miles in diameter, others oblongs 30 miles by 6 or 50 by 20, could hardly mark the rims of volcanoes, for where had ever been volcanic craters so large or oddly shaped?

He didn’t care either for the second most popular hypothesis then around, which was that reef platforms accumulated through sedimentation.

It is improbable in the highest degree that broad, lofty, isolated steep-sided banks of sediment, arranged in groups and lines hundreds of leagues in length, could have been deposited in the central and profoundest parts of the Pacific and Indian Oceans, at an immense distance from any continent, and where the water is perfectly limpid.

But what could explain these huge chains and rings of coral? Some of these island groups stretched hundreds of miles. At least one pair of Pacific archipelagoes, the Low and the Radack, together had hundreds of low, coral isles spread along a line over 4000 miles long, and a similar formation 1500 miles long curved across the Indian Ocean. All of these isles grew atop shallow platforms showed falling away steeply to immense depths. What could have created such long curves and circles of shallow platforms rising from deep water?

Darwin, having pondered for weeks the image of South America rising next to a falling Pacific, saw what now seemed to him obvious: The Pacific’s coral islands did not form on rising mountains; they formed on islands and the high points of large land masses — possibly even continents — that were slowly sinking.

The thought, he said later, came to him in a flash while he was still on the coast pondering charts. Indeed, his notes and correspondence show that he first saw the Pacific reefs not so much as something to be explained, but as evidence of a Pacific subsidence that balanced the rise of the Andes. In his Autobiography (not too many pages before claiming he developed his evolutionary theory through “strict Baconian methods”), he confesses of the coral reef theory that “No other work of mine was begun in so deductive a spirit as this, for the whole theory was thought out on the west coast of South America, before I had seen a true coral reef.”

This was enough to make a Baconian inductivist quake. Yet Darwin could hardly reject his notion of falling islands, for it seemed to explain everything about reefs. In particular, the man who would later ponder variations in finch beaks found it particularly compelling that this idea explained why coral islands, reefs, and atolls took so many variations of ringlike or looping forms. The different reef and atoll forms reflected different stages in the subsidence of the islands on which they took root.

Take a volcanic island, proposed Darwin. Corals would naturally form on the shallows surrounding it. At first this reef, which he called a “fringing reef,” would be thin, and would be directly against the islands shores. But if the island slowly dropped, these corals growing in its surrounding shallows would slowly grow upward, ever thickening but never breaking the surface, to provide a platform for yet more coral. The fringing reef would thicken and broaden, reaching further out to sea.

The fringing reef would soon change, however. Since corals grow more quickly toward the open ocean than toward protected water, the reef would grow faster toward the sea than it would toward the sinking island. As the shore sank, a lagoon would thus form between the reef and the land. The fringing reef would now be a barrier reef — that is, a reef with a lagoon or channel between it and the land it grew around. As time took the island ever further down, the reef would continue to thicken to stay near the surface, and it would continue to grow outward toward the sea. Eventually the island would sink sank beneath the lagoon. Then the barrier reef would become an atoll — a ring of coral matching the former outlines of the island, but now surrounding only a calm lagoon. In the meantime or soon after, the waves might throw enough coral debris and sand atop the reefs to create some of the narrow, strip-shaped islands so common to the Pacific’s coral archipelagos.

To Darwin, this theory not only explained all three types of reefs — fringing, barrier, and atoll; it seemed to be the only theory that satisfactorily explained barrier reefs and atolls reefs at all. Fringing reefs could be explained simply by the fact that corals grew in shallow water. But barrier and atoll reefs required some other explanation, and no other explanation accounted for both of them. Even if you bought that circular atolls had grown on submerged volcanic rims, that idea didn’t explain barrier reefs or more oddly shaped or huge atolls, and it of course asked you to believe that in some areas thousands of these dead volcanoes reached to within 100 fathoms of the surface while none reached above. The other explanations either ignored common reef forms and features or asked us to believe the unbelievable. It was absurd to assert that thousands of mountains all came close to the surface without breaking it; only subsidence could explain these strings of low islands. And only subsidence could plausibly explain barrier reefs and atolls. The logical link was so strong, Darwin believed, that the barrier reefs and atolls in turn provided evidence of subsidence.

This was all from the west coast of South America. When he hopscotched across the Pacific and finally visited atolls and barrier reefs in Tahiti and at the Indian Ocean’s Cocos-Keeling islands, the sight of the formations — particularly the Tahitian island of Moorea, which sat surrounded by its lagoon and barrier reef like an engraving by its matt and frame, as he put it — confirmed to Darwin his vision’s accuracy. “I glad we have visited these islands,” he wrote in his diary, for the coral reefs “rank high amongst the wonderful objects in the world…. [They are] a wonder which does not at first strike the eye of the body, but, after reflection, the eye of reason.” As lovely as the reefs were in pure aesthetic terms (and Darwin keenly appreciated their beauty), they provided for him the even deeper thrill of embodying a deep, time-based pattern apparent only to the imaginative intellect.

This subsidence theory was an audacious idea for a 26-year-old. Conceptually ambitious and blatantly deductive, it begged trouble from all quarters. While challenging the coral-formation theory favored by the new leader of British geology — Lyell — it also aggressively pushed Lyell’s controversial gradualism and speculative method into new territory. As the Beagle rounded Africa and made for England in early 1836, Darwin worried how the senior colleagues be admired, particularly Henslow and Lyell, would receive it.

He was elated when, on his return in fall of 1836, the scientists most important to him, starting with Lyell, found it as thrilling as he did. When he told Lyell of the theory at a lunch at Lyell’s house soon after returning, Lyell became so excited he leapt around the room shouting and laughing, and he immediately dropped his own idea that reefs grew atop mountains that had risen. This idea, he agreed, was far more powerful and beautifully concise. Reefs were not caps atop mountains that had fallen short. They were, as Lyell put it in a letter telling Herschel, “the last efforts of drowning continents to lift their heads above water.”

Lyell immediately arranged to have Darwin read an abstract of the theory at the Geological Society. He warned Darwin that others might not share his own excitement. “Do not flatter yourself that you will be believed till you are growing bald like me, with hard work and vexation at the incredulity of the world.” Yet to Darwin’s delight, he was believed almost immediately. The positive reception began as soon as he read his paper before the Geological Society, in July 1837. Herschel liked it, and Whewell did, too, despite its non-Baconian birth, for the thing worked. Darwin soon won over a wider circle with his presentation of the theory in the Voyage in 1839 and more fully in the 1842 Structure and Distribution of Coral Reefs. Meanwhile, Lyell incorporated Darwin’s subsidence theory into his 1840 edition of Principles, making it quite literally the textbook explanation. Pacific investigations in the 1840s by the British researcher J.B. Jukes and a young James Dwight Dana seemed to confirm the theory. Jukes, having looked extensively at Pacific reefs, said Darwin’s explanation “rises beyond a mere hypothesis into the true theory of coral-reefs.”

Doubters lurked. Some geologists found it difficult to envisage the tectonic movements of which Darwin said subsidence was part. One reviewer called such movements “bold and startling … even to the most hardy of our geologists.” Another scientific reviewer hoped “to find the boldness of [Darwin’s] theories a little modified; and … resting upon a more solid foundation than the supposed undulations of subterranean fluid.” A few people found these objections quite damning. John Cluines Ross, in fact, the owner of Cocos-Keeling atoll, where Darwin saw the atolls that confirmed for him his theory, called it “palaver” and dismissed it out of hand.

These arguments worried Darwin only slightly, for he recognized they came from people who simply didn’t buy the Herschel-Lyell need to speculate. They were fair objections regarding rightly debatable conceptual issues. Of more concern was the way the existing empirical evidence often contradicted his theory and offered it little direct support. As skeptics noted, most of the coral isles studied so far showed much evidence of elevation and no sign of subsidence. Explorers had found corals and other marine fossils atop the taller islands, for instance, but no corresponding terrestrial fossils or structures beneath the surface. And though many (including Darwin) had observed contemporary elevation in action, no one had observed ongoing subsidence. Darwin’s defense — that the recent elevations were cycles amid an overall pattern of marine subsidence, the evidence for which had not been observed because it was hidden under water — couldn’t be backed by anything tangible.

Even more troubling to Darwin was the lack of any discovered deep thickness of continuous coral in the world’s expanding catalogue of examined strata. Geologists had found many thick layers of marine sandstone and sedimentary limestone above ground; why no great thicknesses of coral? When Darwin and Lyell couldn’t resolve this one despite extensive discussion, Darwin had to admit it a “weighty and perplexing” objection.

These and other objections, however, scarcely slowed the theory’s acceptance. By 1850, Darwin’s theory, backed by Lyell and his own expanding base of supporters, became the single most widely accepted theory of coral reef formation. Meanwhile he moved on from it and other geology to work on barnacles and, quietly in the background, his transmutation theory. Even as he did so, the reef theory consolidated its hold. By the time he wrote his Autobiography, in 1876, he could accurately say of The Structure and Distribution of Coral Reefs that it was “thought highly of by scientific men, and the theory therein given is, I think, now well established.” He still got a kick out of its simple power and success; he said it gave him more pleasure than any other theory he’d ever come up with.

For good reason. It’s hard to overstate how vital Darwin’s coral reef theory was in developing his career and thinking. It paved the way, conceptually and methodologically, for everything to come — particularly his transmutation theory. The likenesses startle. Like the transmutation theory, the coral reef theory described how small, virtually unnoticeable changes could create differences of essential type in seemingly immutable forms — and in doing so, account for broad patterns of development and difference.

Thematically, formally, and even psychologically, then, Darwin’s coral reef theory served almost as direct progenitor of his species theory. As perhaps nothing else could have, it prepared him for the conceptually similar but more difficult work on evolution and natural selection. He seems to have needed this dry run — a theoretical foray into the relatively tame territory of rocks and reefs — before pursuing a similar argument on the more perilous species question. He barely thought about the species issue, in fact, until he had finished developing his coral concept. Though the raw zoological data and specimens he collected on the Beagle proved key to his evolution work, they did so only later. His expedition notebooks contain no real contemplation of evolution or variation until he was in Australia, well after his Galapagos visit and when he had just finished recording in his notebook, on the sail from Tahiti to Sydney, the first full abstract of his reef theory. With the abstract sketched out, he made in Australia a few brief notes on species variation, then resumed expanding his reef abstract on the Indian Ocean leg. Returning to London six months later, he told and wrote not of species variation, but of coral reef variation. It was only the following summer that Darwin, who always started a new, subject-specific notebook when he began thinking in earnest on some problem, started his first notebook on “transmutation of species.” That was in July 1837, the same month he had successfully presented his coral reef paper to the Geological Society and begun drafting its full explication in The Structure and Distribution of Coral Reefs. The one theory seemed almost to spring from the other.

The coral reef theory’s subsequent success doubtless helped sustain Darwin during the two decades that he agonized over his transmutation theory. But as he surely recognized (and probably would have liked to forget), another early theory of his also shared the reef theory’s conceptual hallmarks: Glen Roy. His botched explanation of that valley’s parallel roads, published two years after his initial coral reef presentation, also sought to explain a geologic mystery by proposing a series of changes over long periods. It too sprang from a vision of rising and falling land masses. Yet in the decade after he published it, his Glen Roy theory fell to Louis Agassiz and became Darwin’s most painful humiliation. (“Eheu! Eheu!”) If his reef theory’s success buoyed him in his evolution work, the Glen Roy debacle served a sober warning. Indeed, the Glen Roy reversal gave ample reason to doubt his coral reef theory. He had erred at Glen Roy both by overlooking contradictory evidence (the streams that he missed but Agassiz found) and by downplaying the lack of direct confirming evidence, such as the missing marine fossils, as a type of evidence that was simply unlikely to be found. In his coral reef theory he chose to overlook the common signs of elevation and dismiss the absence of direct evidence of subsidence. Might these prove to be errors as fatal as those he made at Glen Roy? Darwin seemed to set aside such questions as the decades passed. But they were right there for anyone else to pick up.